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1 /*****************************************************************************
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2 intersectBed.h
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3
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4 (c) 2009 - Aaron Quinlan
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licenced under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #ifndef INTERSECTBED_H
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13 #define INTERSECTBED_H
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14
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15 #include "bedFile.h"
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16 #include "chromsweep.h"
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17 #include "api/BamReader.h"
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18 #include "api/BamWriter.h"
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19 #include "api/BamAux.h"
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20 #include "BamAncillary.h"
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21 using namespace BamTools;
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22
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23
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24 #include <vector>
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25 #include <iostream>
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26 #include <fstream>
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27 #include <stdlib.h>
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28 using namespace std;
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29
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30
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31
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32 class BedIntersect {
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33
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34 public:
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35
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36 // constructor
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37 BedIntersect(string bedAFile, string bedBFile, bool anyHit,
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38 bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap,
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39 float overlapFraction, bool noHit, bool writeCount, bool sameStrand, bool diffStrand,
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40 bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput, bool isUncompressedBam,
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41 bool sortedInput);
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42
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43 // destructor
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44 ~BedIntersect(void);
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45
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46 private:
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47
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48 //------------------------------------------------
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49 // private attributes
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50 //------------------------------------------------
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51 string _bedAFile;
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52 string _bedBFile;
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53
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54 bool _writeA; // should the original A feature be reported?
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55 bool _writeB; // should the original B feature be reported?
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56 bool _writeOverlap;
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57 bool _writeAllOverlap;
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58
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59 bool _sameStrand;
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60 bool _diffStrand;
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61 bool _reciprocal;
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62 float _overlapFraction;
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63
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64 bool _anyHit;
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65 bool _noHit;
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66 bool _writeCount; // do we want a count of the number of overlaps in B?
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67 bool _obeySplits;
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68 bool _bamInput;
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69 bool _bamOutput;
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70 bool _isUncompressedBam;
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71 bool _sortedInput;
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72 bool _printable;
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73
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74 // instance of a bed file class.
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75 BedFile *_bedA, *_bedB;
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76
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77 //------------------------------------------------
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78 // private methods
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79 //------------------------------------------------
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80 void IntersectBed(istream &bedInput);
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81
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82 void IntersectBed();
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83
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84 void IntersectBam(string bamFile);
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85
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86 bool processHits(const BED &a, const vector<BED> &hits);
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87
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88 bool FindOverlaps(const BED &a, vector<BED> &hits);
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89
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90 bool FindOneOrMoreOverlap(const BED &a);
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91
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92 void ReportOverlapDetail(int overlapBases, const BED &a, const BED &b, CHRPOS s, CHRPOS e);
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93
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94 void ReportOverlapSummary(const BED &a, const int &numOverlapsFound);
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95
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96 };
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97
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98 #endif /* INTERSECTBED_H */
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